Identification of respiratory pathogens in the mouth has led researchers to hypothesize that a relationship exists between the oral cavity and pulmonary infections. A common complication of allogeneic peripheral blood stem cell transplant is infection and pneumonia. Identification of potential pathogens in the oral cavity of allogeneic stem cell patients could indicate a similar association between oral pathogens and infection. This study population (n=50) was composed of adult patients who had been scheduled to receive an allogeneic stem cell transplant (ASCT). Forty-five patients were consented and received an ASCT. Saliva specimens, dental plaque and mucosal brushings was collected at the three different times during the patients treatment and recovery. Additional oral specimens was obtained from patients who develop respiratory signs or symptoms that required an inpatient or intensive care unit admission. Patients were followed and assessed for respiratory signs, symptoms, inpatient or ICU admission until day 100 post-transplant.